A cashiered senior official in the Pentagon’s inspector general office ended years of anonymous complaints this weekend, giving interviews about his former employer’s handling of whistleblowers in key national security controversies, including the Edward Snowden and Thomas Drake cases.

John Crane, 60, who spent 25 years in government before he was fired as an assistant Defense Department inspector general in 2013, went public with a series of accusations that key officials in the watchdog’s office retaliated against whistleblowers, destroyed permanent records and altered audits under political pressure.

He has filed those charges with the Office of Special Counsel, which so far has referred one to the Justice Department for detailed investigation, though others may soon follow.

In an interview with Government Executive on Sunday, Crane challenged the criticism by many top U.S. officials who say Edward Snowden, the former Booz Allen Hamilton employee who worked as a National Security Agency contractor, could have taken his complaint through official channels. In 2013, Snowden flew to Hong Kong, leaked classified documents exposing U.S. surveillance programs and ultimately took refuge in Russia.

“Edward Snowden and his decision not to go through the whistleblower process indicate a larger failure within DOD IG,” Crane said. “Snowden did not go through the IG because he saw what had happened to Thomas Drake,” he added.

The Drake case, also a hallmark in the whistleblower community, involved the Justice Department’s prosecution of an NSA senior executive in 2010 under the Espionage Act for speaking to the Baltimore Sun about wasteful NSA programs going back a decade. The government eventually dropped the case after public outcry and skepticism from a federal judge, and Drake pleaded guilty to a lesser charge.

Crane, in the meantime, thought he had witnessed retaliation against Drake by DoD IG officials Lynne Halbrooks (now a private attorney) and General Counsel Henry C. Shelley Jr., along with the destruction of documents relevant to the case more than a decade ago when Crane was handling Drake’s disclosures to the IG’s office. Crane reported that to the Office of Special Counsel, which in March referred the case to Justice Office of Inspector General.

Crane is now a stay-at-home father living in McLean, Va., while fighting to get his job back. He continues to meet with the Office of Special Counsel as it reviews several other complaints against the DOD IG.

Crane and his attorney have spent hours testifying to lawmakers, one result being language in the pending National Defense Authorization Act that would clarify whistleblower protections against retaliation and require a Government Accountability Office review of the Defense IG’s conduct.

The Senate version, said Tom Devine, the legal director of the Government Accountability Project who is representing Crane, calls for GAO to perform “a systematic review of the Pentagon IG’s whistleblower program.” That’s based in part on “Crane’s disclosures of contradictory approaches to law enforcement by Obama administration leaders,” Devine said. “Mr. Crane blew the whistle because he perceived a systematic mission breakdown in the Pentagon OIG system.”

The Senate bill calls for a “systematic makeover of the military whistleblower protection act for members of the armed services,” Divine said. “It is landmark free speech legislation if it survives the [House-Senate] conference.” The House version contains a more limited provision, he added, that would modernize legal burdens of proof to give soldiers the same whistleblower rights as civilian employees.

Other disclosures Crane has filed with OSC include allegations Halbooks and Shelley made “false statements under oath, using a fictional narrative to have me removed,” he said. Halbrooks is also accused of softening a report on the Pentagon IG’s handling of arrangements in the investigation of whether then-CIA Director Leon Panetta and Defense Undersecretary for Intelligence Michael Vickers broke classification rules by revealing the name of the Navy Seal Team 6 leader to Hollywood filmmakers making the movie “Zero Dark Thirty.”

Among the other charges being considered by the OSC is whether Crane was thwarted by superiors during an investigation related to the 2010 disclosures by Col. Mark Fassl of patient neglect at a U.S.-funded military hospital in Afghanistan, which became the subject of Capitol Hill hearings.

Staff serving under current acting Defense IG Glenn Fine have been meeting with the OSC on Crane’s issues. “We are reviewing the language and directives in” the Senate NDAA bill, Kathie Scarrah, director of legislative affairs and communications at DOD IG's office, told Government Executive. As for Crane’s allegations, her office has asked the Justice Department’s Office of Inspector General “to initiate‎ an independent investigation into the allegations. [The IG’s office] will cooperate fully and looks forward to the results of that investigation.”

Former acting Defense IG Halbrooks, now a partner at the law firm of Holland & Knight, told Government Executive in an email, “During my time at DOD OIG I strongly supported the rights of whistleblowers throughout the Department of Defense. I welcome the opportunity to cooperate with any government investigation into these false allegations.”

What are Crane’s goals in continuing these disclosures? “The whistleblower program that I set up at DOD IG has been characterized as the gold standard for the federal government,” he said. “But in light of GAO investigations, in light of the current language in the NDAA, that is no longer the case. Outside advocacy groups and Congress recognized serious problems at DOD IG,” Crane added. “Should Mr. Fine want to return it to the gold standard, I would be willing to help him.”

Correction: The initial version of this story incorrectly characterized the action taken by the Office of Special Counsel in March. The story has been corrected.